Package picard.analysis.artifacts
Enum Transition
- java.lang.Object
-
- java.lang.Enum<Transition>
-
- picard.analysis.artifacts.Transition
-
- All Implemented Interfaces:
Serializable
,Comparable<Transition>
public enum Transition extends Enum<Transition>
Enum representation of a transition from one base to any other.
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description protected static class
Transition.Base
-
Field Summary
Fields Modifier and Type Field Description protected static int[]
baseIndexMap
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static Transition[]
altValues()
Like values(), but ignores the ref:ref "transitions".char
call()
Gets the call for the transition.Transition
complement()
Return the complementary transition.char
ref()
Gets the reference for the transition.String
toString()
static Transition
transitionOf(char ref, char call)
Gets a the enum representing the transition from a 'reference' to a 'call' base.static Transition
valueOf(String name)
Returns the enum constant of this type with the specified name.static Transition[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
-
-
-
Enum Constant Detail
-
AtoA
public static final Transition AtoA
-
AtoC
public static final Transition AtoC
-
AtoG
public static final Transition AtoG
-
AtoT
public static final Transition AtoT
-
CtoA
public static final Transition CtoA
-
CtoC
public static final Transition CtoC
-
CtoG
public static final Transition CtoG
-
CtoT
public static final Transition CtoT
-
GtoA
public static final Transition GtoA
-
GtoC
public static final Transition GtoC
-
GtoG
public static final Transition GtoG
-
GtoT
public static final Transition GtoT
-
TtoA
public static final Transition TtoA
-
TtoC
public static final Transition TtoC
-
TtoG
public static final Transition TtoG
-
TtoT
public static final Transition TtoT
-
-
Method Detail
-
values
public static Transition[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (Transition c : Transition.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
-
valueOf
public static Transition valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
-
transitionOf
public static Transition transitionOf(char ref, char call)
Gets a the enum representing the transition from a 'reference' to a 'call' base.For example, a transtion from 'A' to 'T' would return
AtoT
.- Parameters:
ref
- reference base (one of of {A, C, T, G}).call
- call base (one of of {A, C, T, G}).- Returns:
- enum representation for the transition.
-
altValues
public static Transition[] altValues()
Like values(), but ignores the ref:ref "transitions".
-
complement
public Transition complement()
Return the complementary transition. Both ref and call must be complemented.
-
ref
public char ref()
Gets the reference for the transition.
-
call
public char call()
Gets the call for the transition.
-
toString
public String toString()
- Overrides:
toString
in classEnum<Transition>
-
-